These projects are in a usable form. Packages have been developed following
RECON’s standards, are fully functional, documented and tested, and have been
released on CRAN.
distcrete
Discretized probability distributions.
EpiEstim
Quantifying transmissibility throughout an epidemic from incidence time series.
earlyR
Estimation of infectiousness in the early stage of an outbreak
epicontacts
Handling, visualisation and analysis of epidemiological contacts.
epitrix
Small helpers and tricks for epidemics analysis
incidence
Computation, handling, visualisation and simple modelling of incidence.
aweek
Convert dates to arbitrary week definitions including epiweek, isoweek, and more
outbreaker2
Modular framework for outbreak reconstruction.
outbreaks
Collection of outbreak data.
projections
Projections of future incidence
RECON learn
Open training platform for epidemics analysis
epiflows
Visualisation and analysis of passenger flows
The RECON packages listed below are still in development. They may be functional
already, but a stable version has yet to be released.
bpmodels
Analysis of transmission chains using branching processes.
branchr
R Estimation from Cluster Sizes
cleanr
Rationalised and reproducible data cleaning.
drat
Install devel versions of RECON packages by default.
deployer
Portable environment for epidemics analysis
dibbler
Investigation of food-borne disease outbreaks.
docker
Docker images for RECON packages
epicontacts.ui
Graphical user interface for epicontacts
epimaps
Helpers and wrappers for mapping diseases
epimatch
Finding matching patient records across tabular data sets.
gisfirstaid
Tutorials and code gists for mapping infectious diseases
incidence.ui
Graphical user interface for incidence
linelist
Tools to Import and Tidy Case Linelist Data
nomad
Pack up R to take away
recontools
Tools to develop RECON packages
recon.ui
Template shiny GUI for RECON packages
reportfactory
Facilitate rmarkdown workflows
vimes
Visualisation and Monitoring of Epidemics, including some outbreak detection algorithms.
The packages listed below mostly predate RECON, but have been authored by RECON
members and are relevant for infectious disease epidemiology.
OutbreakTools
Basic analysis and visualisation of complex line-list data (to be replaced by incidence and epicontacts).
EpiJSON
Implementation of a generic json format for case outbreak data.
repijson
R package implementing EpiJSON format.
outbreaker
Inferring transmission chains using temporal and genetic information.
surveillance
Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena
DSAIDE
Dynamical Systems Approach to Infectious Disease Epidemiology - a Shiny/R based teaching tool.
EpiModel
Mathematical Modeling of Infectious Disease Dynamics
treedater
Molecular clock dating of pathogen phylogenies.
skygrowth
Phylodynamic inference of effective population size through time.